4OBZ

Structure of Cathepsin D with inhibitor 2-(3,4-dimethoxyphenyl)-N-[N-(4-methylbenzyl)carbamimidoyl]acetamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report



Literature

Structure-based optimization of non-peptidic Cathepsin D inhibitors.

Gradler, U.Czodrowski, P.Tsaklakidis, C.Klein, M.Werkmann, D.Lindemann, S.Maskos, K.Leuthner, B.

(2014) Bioorg Med Chem Lett 24: 4141-4150

  • DOI: 10.1016/j.bmcl.2014.07.054
  • Primary Citation of Related Structures:  
    4OBZ, 4OC6, 4OD9

  • PubMed Abstract: 
  • We discovered a novel series of non-peptidic acylguanidine inhibitors of Cathepsin D as target for osteoarthritis. The initial HTS-hits were optimized by structure-based design using CatD X-ray structures resulting in single digit nanomolar potency in the biochemical CatD assay ...

    We discovered a novel series of non-peptidic acylguanidine inhibitors of Cathepsin D as target for osteoarthritis. The initial HTS-hits were optimized by structure-based design using CatD X-ray structures resulting in single digit nanomolar potency in the biochemical CatD assay. However, the most potent analogues showed only micromolar activities in an ex vivo glycosaminoglycan (GAG) release assay in bovine cartilage together with low cellular permeability and suboptimal microsomal stability. This new scaffold can serve as a starting point for further optimization towards in vivo efficacy.


    Organizational Affiliation

    Merck KGaA, Merck Serono Research, Small Molecule Platform, Frankfurter Str. 250, 64293 Darmstadt, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cathepsin D light chainAC103Homo sapiensMutation(s): 0 
Gene Names: CPSDCTSD
EC: 3.4.23.5
Find proteins for P07339 (Homo sapiens)
Explore P07339 
Go to UniProtKB:  P07339
NIH Common Fund Data Resources
PHAROS  P07339
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cathepsin D heavy chainBD243Homo sapiensMutation(s): 0 
Gene Names: CPSDCTSD
EC: 3.4.23.5
Find proteins for P07339 (Homo sapiens)
Explore P07339 
Go to UniProtKB:  P07339
NIH Common Fund Data Resources
PHAROS  P07339
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2S4
Query on 2S4

Download CCD File 
B
2-(3,4-dimethoxyphenyl)-N-[N-(4-methylbenzyl)carbamimidoyl]acetamide
C19 H23 N3 O3
LDSKOSCPBKZJCO-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2S4IC50:  1900   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 230.34α = 90
b = 42.454β = 90
c = 73.216γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2014-09-10
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary